Transcript madam_4_0

Microarray Data Management
Jianwei (Jerry) Li
April 2004
test
1
Microarray Data Flow
Printer
Scanner
.tiff Image File
Image
Analysis
Raw Gene
Expression Data
Gene Annotation
AGED
Normalization
/ Filtering
Normalized Data
with Gene
Annotation
Others…
MAD
Database
Database
Database
Expression
Analysis
Data Entry /
Management
Interpretation of
Analysis Results
test
2
Microarray Experiment and Annotation
Control
Test
Obtain RNA
Samples
Prepare Fluorescently
Labeled Probes
Hybridize, Wash
Scanning
MADAM
test
3
Requirements of MADAM
 Communicates with a DBMS.
 Uploads microarray information to database
with a convenient way.
 Allows users to view the information.
 Retrieves the information and converts it to
a data format for analysis.
 Checks errors for the data entries.
 Starts other tools to manipulate the data.
test
4
Functions of MADAM
Data Entry
Other Tools
Data Display
Data Retrieve
MADAM
Protista
test
5
Microarray Database Schema
Slide
Slide_name
id
slide_type
config_id
slide_lot
bar_code
run_id
storage_id
test
6
Conceptual Schema: MAD
Clone
Slide
Slide_type
New_plate
Spot
Gene
Hyb
Study
Experiment
Expression
Expt_prob
e
Probe
Scan
Probe_source
Analysis
Protocol
Normalize
test
PCR
Primer_pair
Primer
7
Interface of MADAM
Tool Bar
Navigation Panel
Working Panel
Log Panel
test
8
Data Entry …
test
9
Procedures of Data Entry
1. Enter an organism name using
New Organism Window.
2. Upload your plate and PCR
information with PCR Score.
3. Insert study information with
Study page.
4. Insert probe data with Probe and
Probe Source pages.
5. Use other pages ...
test
10
PCR File Format - 1
Type 1: 7-Column Gene or Clone
Feat Name / Locus
Primer 1 Sequence
Primer 1 Name
Primer 2 sequence Amplified Value
Primer 2 Name
test
Length
11
PCR File Format - 2
Type 2: 8-Column Gene or Clone
Feat Name
Primer 1 Sequence
Primer 1 Name
Primer 2 sequence
Primer 2 Name
test
Length
Amplified Value
Locus
12
PCR File Format - 3
Type 3: Oligo
Feat Name
Locus
5' end
Primer Name
Sequence
test
Amplified Value
3' end
Tm
13
Procedures of Data Entry
1. Enter an organism name using
New Organism Window.
2. Upload your plate and PCR
information with PCR Score.
3. Insert study information with
Study page.
4. Insert probe data with Probe and
Probe Source pages.
5. Use other pages ...
test
14
Data Entry With Study Page
a chemical or factor that is
used for treatment in a
study (H2O, light, NaCl).
Time : 10 : Hour
Time : 5 : Day
Temperature : 30 : ºC
10% NaCl : 100 : ml
test
15
Introduction of Slide Type


Not the type of slide manufacturers produced.
Array type that describe how the array was constructed.
test
16
Interface of Slide Type
test
17
Format of Slide Name
cag005a0036
Project Name
Glass Type
Consequential Number
Config_id
config
id
machine
slide_type
pins_x
pins_y
dist_x
dist_y
…
test
18
Functions of Other Pages
inserts the locations of the
image files and scan
parameters into database.
Scan
uploads the intensities
(mev or tav files) of an
experiment to database.
Expression
saves normalized
intensities to database
(unavailable).
Analysis
test
19
Data Report …
test
20
Data Retrieve …
test
21
Data Retrieve with Miner
select experiment.
check what
amplified value to
be zero.
select output file
format.
provide file name.
start to retrieve.
test
22
mev and tav File Format
Spot positions
Intensities
Backgrounds
test
Flags
23
MGED, MIAME, and MAGE-ML
 Microarray Gene Expression Data Society
Goal: facilitate microarray data exchange between scientists
 Working Groups:
* Experiment description standards (MIAME)
* Data exchange format (MAGE-ML)
* Ontologies for sample description
 Minimal Information About Microarray Experiments.
* Minimal description of a set of microarray experiments.
 MicroArray Gene Expression Markup Language.
* XML based means of exchanging microarray data
test
24
ArrayExpress: Public Repository
test
25
MIAMExpress: Data Submission Tool
test
26
MAGE-ML Nodes
slide: how a slide is generated
slide type
process of making slide
probe sequence
spots on slide
researchers who conduct the experiments
probe source
study
hybridization
expression intensity
how to measure intensities
test
27
MAGE-ML Export with Madam
provide person’s info.
indicate the role (submitter,
researcher, …) of the person.
select an experiment to be
written out.
provide a file name.
start the writing.
test
28
MAGE-ML Output of Experiment
test
29
Other tools …
test
30
Query Window
type SQL code.
click the Submit
button.
view the query results.
save the query results.
test
31
Experiment Designer
set the number of
samples (probes).
indicate the compare
relationship with
arrows or chart.
save the picture.
test
32
Express Converter
for GenePix, Image,
ScanArray, TAV, and
MEV files.
set a number of files to
be converted.
output files have the
same names & paths
with diff. extension.
change the file names
or paths if you want.
start converting.
test
33
Functions of MADAM
Data Entry
Other Tools
Data Display
Data Retrieve
MADAM
Protista
test
34
Acknowledgements
TIGR Microarray Software Team
John Quackenbush
Nirmal Bhagabati
John Braisted
Tracey Currier
Eleanor Howe
Jerry Li
Wei Liang
Alexander I. Saeed
Vasily Sharov
Mathangi Thaiagarjian
Joseph White
test
35